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Coexpression cluster:C1619: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002619!1.74e-91!22;UBERON:0001950!5.05e-91!20;UBERON:0000956!1.98e-80!25;UBERON:0000203!1.98e-80!25;UBERON:0001869!9.38e-76!32;UBERON:0001893!3.74e-71!34;UBERON:0002791!7.01e-69!32;UBERON:0003528!1.10e-64!34;UBERON:0002020!1.10e-64!34;UBERON:0001017!2.03e-61!81;UBERON:0002780!1.68e-58!41;UBERON:0001890!1.68e-58!41;UBERON:0003080!1.68e-58!41;UBERON:0006240!1.68e-58!41;UBERON:0001016!8.16e-55!89;UBERON:0000955!1.86e-51!68;UBERON:0006238!1.86e-51!68;UBERON:0000073!1.24e-48!53;UBERON:0002616!1.24e-48!53;UBERON:0001049!8.22e-46!56;UBERON:0005068!8.22e-46!56;UBERON:0006241!8.22e-46!56;UBERON:0007135!8.22e-46!56;UBERON:0003056!4.42e-38!61;UBERON:0000200!7.66e-33!6;UBERON:0003075!6.77e-30!82;UBERON:0007284!6.77e-30!82;UBERON:0002346!2.72e-28!86;UBERON:0002021!3.49e-28!5;UBERON:0001872!6.09e-28!5;UBERON:0004121!4.64e-26!171;UBERON:0000924!4.64e-26!171;UBERON:0006601!4.64e-26!171;UBERON:0010371!1.39e-22!104;UBERON:0011216!1.26e-21!223;UBERON:0007023!4.18e-20!114;UBERON:0001871!1.42e-19!6;UBERON:0010314!1.54e-18!132;UBERON:0001870!4.11e-17!3;UBERON:0002702!3.35e-12!2;UBERON:0002771!3.55e-12!2;UBERON:0000477!2.11e-10!373;UBERON:0000025!5.00e-10!192;UBERON:0000349!7.05e-10!5;UBERON:0000064!3.29e-09!218;UBERON:0004111!4.51e-07!240;UBERON:0002902!5.57e-07!1;UBERON:0009899!5.57e-07!1;UBERON:0002581!5.89e-07!1;UBERON:0003112!7.39e-07!1;UBERON:0011158!7.39e-07!1;UBERON:0003128!7.39e-07!1;UBERON:0001703!7.39e-07!1;UBERON:0002241!7.39e-07!1;UBERON:0004761!7.39e-07!1;UBERON:0009617!7.39e-07!1
|ontology_enrichment_uberon=UBERON:0002619!1.74e-91!22;UBERON:0001950!5.05e-91!20;UBERON:0000956!1.98e-80!25;UBERON:0000203!1.98e-80!25;UBERON:0001869!9.38e-76!32;UBERON:0001893!3.74e-71!34;UBERON:0002791!7.01e-69!32;UBERON:0003528!1.10e-64!34;UBERON:0002020!1.10e-64!34;UBERON:0001017!2.03e-61!81;UBERON:0002780!1.68e-58!41;UBERON:0001890!1.68e-58!41;UBERON:0003080!1.68e-58!41;UBERON:0006240!1.68e-58!41;UBERON:0001016!8.16e-55!89;UBERON:0000955!1.86e-51!68;UBERON:0006238!1.86e-51!68;UBERON:0000073!1.24e-48!53;UBERON:0002616!1.24e-48!53;UBERON:0001049!8.22e-46!56;UBERON:0005068!8.22e-46!56;UBERON:0006241!8.22e-46!56;UBERON:0007135!8.22e-46!56;UBERON:0003056!4.42e-38!61;UBERON:0000200!7.66e-33!6;UBERON:0003075!6.77e-30!82;UBERON:0007284!6.77e-30!82;UBERON:0002346!2.72e-28!86;UBERON:0002021!3.49e-28!5;UBERON:0001872!6.09e-28!5;UBERON:0004121!4.64e-26!171;UBERON:0000924!4.64e-26!171;UBERON:0006601!4.64e-26!171;UBERON:0010371!1.39e-22!104;UBERON:0011216!1.26e-21!223;UBERON:0007023!4.18e-20!114;UBERON:0001871!1.42e-19!6;UBERON:0010314!1.54e-18!132;UBERON:0001870!4.11e-17!3;UBERON:0002702!3.35e-12!2;UBERON:0002771!3.55e-12!2;UBERON:0000477!2.11e-10!373;UBERON:0000025!5.00e-10!192;UBERON:0000349!7.05e-10!5;UBERON:0000064!3.29e-09!218;UBERON:0004111!4.51e-07!240;UBERON:0002902!5.57e-07!1;UBERON:0009899!5.57e-07!1;UBERON:0002581!5.89e-07!1;UBERON:0003112!7.39e-07!1;UBERON:0011158!7.39e-07!1;UBERON:0003128!7.39e-07!1;UBERON:0001703!7.39e-07!1;UBERON:0002241!7.39e-07!1;UBERON:0004761!7.39e-07!1;UBERON:0009617!7.39e-07!1
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,2.66447,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,1.20439,0.963929,0.395009,0.287891,0.969147,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.758594,0.417272,0.195238,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,1.34093,0.293154,0.934302,0.755403,0.873042,1.18161,0.0719601,0.963115,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,0.211081,1.7889,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,0.577088,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,2.90914,0.0214572
}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1619_medulloblastoma_occipital_duodenum_Neural_parietal_temporal_Neurons



Phase1 CAGE Peaks

Hg19::chr11:123276174..123276187,+p@chr11:123276174..123276187
+
Hg19::chr2:162272716..162272753,+p3@TBR1
Hg19::chr2:162272889..162272915,+p2@TBR1
Hg19::chr2:162272970..162272981,+p10@TBR1
Hg19::chr2:162276951..162276955,+p@chr2:162276951..162276955
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell2.67e-118
neuron9.81e-096
neuroblast9.81e-096
electrically signaling cell9.81e-096
Uber Anatomy
Ontology termp-valuen
regional part of cerebral cortex1.74e-9122
neocortex5.05e-9120
cerebral cortex1.98e-8025
pallium1.98e-8025
cerebral hemisphere9.38e-7632
telencephalon3.74e-7134
regional part of telencephalon7.01e-6932
brain grey matter1.10e-6434
gray matter1.10e-6434
central nervous system2.03e-6181
regional part of forebrain1.68e-5841
forebrain1.68e-5841
anterior neural tube1.68e-5841
future forebrain1.68e-5841
nervous system8.16e-5589
brain1.86e-5168
future brain1.86e-5168
regional part of nervous system1.24e-4853
regional part of brain1.24e-4853
neural tube8.22e-4656
neural rod8.22e-4656
future spinal cord8.22e-4656
neural keel8.22e-4656
pre-chordal neural plate4.42e-3861
gyrus7.66e-336
neural plate6.77e-3082
presumptive neural plate6.77e-3082
neurectoderm2.72e-2886
occipital lobe3.49e-285
parietal lobe6.09e-285
ectoderm-derived structure4.64e-26171
ectoderm4.64e-26171
presumptive ectoderm4.64e-26171
ecto-epithelium1.39e-22104
organ system subdivision1.26e-21223
adult organism4.18e-20114
temporal lobe1.42e-196
structure with developmental contribution from neural crest1.54e-18132
frontal cortex4.11e-173
middle frontal gyrus3.35e-122
middle temporal gyrus3.55e-122
anatomical cluster2.11e-10373
tube5.00e-10192
limbic system7.05e-105
organ part3.29e-09218
anatomical conduit4.51e-07240
occipital pole5.57e-071
pole of cerebral hemisphere5.57e-071
postcentral gyrus5.89e-071
olfactory region7.39e-071
primary subdivision of skull7.39e-071
cranium7.39e-071
neurocranium7.39e-071
chondrocranium7.39e-071
cartilaginous neurocranium7.39e-071
head paraxial mesoderm7.39e-071


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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